run_metadata: 30746

This data as json

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30746	SRR28348607	SRX23954674	SRS20755104	SRP495302	PRJNA1088122	Decoding the molecular cellular and functional heterogeneity of zebrafish intracardiac nervous system	GSE261619	Transcriptome Analysis	In this project we present a comprehensive taxonomy of the intracardiac nervous system IcNS utilizing single cell RNA sequencing anatomical studies and electrophysiological techniques. Overall design: For single cell sequencing experiments 25 Tgelavl3:eGFP previously known as HuC:GFP of 5 mpf animal were used from both sexes for the first set and 25 Tgelavl3:eGFP of 11 mpf and 10 Tgnbt:DsRed of 22 mpf animals from both sexes were used for the second set. Cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11 v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.		pubmed:39632839		Tgelavl3:eGFP Tgnbt:DsRed	GSM8147512		source name:atrium\|tissue:atrium\|genotype:Tgelavl3:eGFP Tgnbt:DsRed\|geo loc name:missing\|collection date:missing	Tgelavl3:eGFP Tgnbt:DsRed	The demultiplexing barcoded processing gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger	atrium		Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish viability indicator dyes Sytox Blue Invitrogen Cat No. S34857 and Dycle Ruby Invitrogen Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics	Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle pH7.5 at 28°C ±1°C in groups of 20 animals per 2.8L.	tissue:atrium\|genotype:Tgelavl3:eGFP Tgnbt:DsRed	GSM8147512	GSM8147512: Tgelavl3:eGFP Tgnbt:DsRed; Danio rerio; RNA Seq	GSM8147512 r1	GSM8147512	1	Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish viability indicator dyes Sytox Blue Invitrogen Cat No. S34857 and Dycle Ruby Invitrogen Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP495302		loader:fastq load.py	CP030_S1_L004_I1_001.fastq.gz CP030_S1_L004_I2_001.fastq.gz CP030_S1_L004_R1_001.fastq.gz CP030_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	86914563102.0	391507041.0	GSM8147512 r1	0:10 1:10 2:101 3:101	A:23707102309;C:15625825731;G:14915197158;T:24834868356;N:1428728	10	10	101	101	23707102309	15625825731	14915197158	24834868356	1428728	SRX23954674	SRS20755104	SRA1824602	Neurology & TAUB Institute, Columbia University	Neurology & TAUB Institute, Columbia University	2	0.0	0.94374	0.0	0.12308	1.0	0.82055		0.55544	101	101	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2024-03-14	Undetermined	Adult	Heart	Cardiovascular System